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    27 repositories

    • risk

      Public
      RISK: a next-generation tool for biological network annotation and visualization
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Feb 2, 2026Feb 2, 2026

    • PythonProteomics

      Public
      A collection of available Python tools for Proteomics analysis
      MIT License
      •13•67•0•0•Updated Jan 31, 2026Jan 31, 2026

    • Labnotebook-Template

      Public
      TeX
      •1•0•0•0•Updated Jan 31, 2026Jan 31, 2026

    • DIAlignR

      Public
      This is a R package for alignment of DIA mass-spec data
      R
      •7•12•2•1•Updated Jan 31, 2026Jan 31, 2026

    • msproteomicstools

      Public
      Some hopefully useful tools for mass spectrometry applied to proteomics
      Python
      •
      Other
      •40•0•0•0•Updated Jan 31, 2026Jan 31, 2026

    • dia-pasef

      Public
      Scripts for DIA-Pasef
      Python
      •12•5•1•3•Updated Jan 31, 2026Jan 31, 2026

    • test_repository

      Public
      To test and learn git
      Python
      •2•1•2•4•Updated Jan 31, 2026Jan 31, 2026

    • srmcollider

      Public
      Computes interferences in SRM (Selected Reaction Monitoring) experiments.
      Python
      •4•0•0•0•Updated Jan 31, 2026Jan 31, 2026

    • containers

      Public
      Bioinformatics containers
      Jupyter Notebook
      •
      Apache License 2.0
      •261•0•0•0•Updated Jan 31, 2026Jan 31, 2026

    • thesis-template

      Public
      A LaTeX template for academic theses
      TeX
      •
      MIT License
      •2•1•0•0•Updated Jan 31, 2026Jan 31, 2026

    • OpenMS

      Public
      The codebase of the OpenMS project
      C++
      •
      Other
      •380•1•0•3•Updated Jan 31, 2026Jan 31, 2026

    • massdash

      Public
      MassDash: A web-based dashboard for streamlined DIA-MS visualization, analysis, prototyping, and optimization
      visualizationmass-spectrometrydata-independent-acquisition
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •3•21•16•5•Updated Jan 12, 2026Jan 12, 2026

    • pyprophet

      Public
      PyProphet: Semi-supervised learning and scoring of OpenSWATH results.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •21•0•1•1•Updated Dec 19, 2025Dec 19, 2025

    • easypqp

      Public
      EasyPQP: Simple library generation for OpenSWATH
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •14•0•0•0•Updated Dec 12, 2025Dec 12, 2025

    • easypqp-rs

      Public
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Dec 11, 2025Dec 11, 2025

    • documentation

      Public
      This repository contains the website documentation for OpenSWATH.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •13•0•0•0•Updated Dec 11, 2025Dec 11, 2025

    • oDIAFlow

      Public
      An Open Nextflow pipeline for analyzing DIA-MS (Data-Independent Acquisition Mass Spectrometry) data.
      Nextflow
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Nov 19, 2025Nov 19, 2025

    • redeem

      Public
      Repository for Deep Learning Models for Mass Spectrometry written in Rust
      Rust
      •2•1•0•0•Updated Aug 19, 2025Aug 19, 2025

    • arycal

      Public
      ARYCAL: across run DIA-MS extracted ion chromatogram alignment written in Rust
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Aug 19, 2025Aug 19, 2025

    • diffusion-deconvolution-dia-msms-data

      Public
      🚀 Winner of the Donnelly Centre Innovation and Commercialization award: Apply diffusion models to deconvolute highly multiplexed DIA-MS/MS data by conditioning …
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •11•11•5•3•Updated Apr 4, 2025Apr 4, 2025

    • massformer

      Public
      Tandem Mass Spectrum Prediction with Graph Transformers
      Python
      •
      BSD 2-Clause "Simplified" License
      •32•99•2•0•Updated Aug 26, 2024Aug 26, 2024

    • PaPrInfer

      Public
      These are all the code that is associated with the project IDPicker vs EPIFANY
      Python
      •1•0•0•0•Updated Jul 6, 2024Jul 6, 2024

    • OpenSWATHIDPIcker

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Oct 24, 2022Oct 24, 2022

    • Aparna_Srinivasan_MS_Thesis_2022

      Public
      Aparna's MSc thesis related scripts
      Python
      •0•0•0•0•Updated Sep 29, 2022Sep 29, 2022

    • diaproteomics

      Public
      Automated quantitative analysis of DIA proteomics mass spectrometry measurements.
      Nextflow
      •
      MIT License
      •12•1•0•0•Updated Apr 27, 2021Apr 27, 2021

    • DrawAlignR

      Public
      An R package for the visualization of aligned ms2 chromatograms.
      R
      •
      MIT License
      •4•5•0•0•Updated Apr 9, 2020Apr 9, 2020

    • mstools

      Public
      R
      •1•1•0•0•Updated Feb 4, 2020Feb 4, 2020